Functional significance of commonly regulated genes in mechanically and chemically induced retinal ganglion cell death in rat eyes by Masaaki Kageyama, Koji Ohashi, Takashi Ota

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Leveraging hybrid 1D-CNN and RNN approach for classification of brain cancer gene expression by Heba M. Afify, Kamel K. Mohammed, Aboul Ella Hassanien

Subjects: “…Curated microarray database (CuMiDa)…”
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Cold-inducible RNA-binding protein is associated with subtype-specific breast cancer patient outcomes by Matthew Dankner, Veronique Ouellet, Jakob Lafon, Rima Ezzeddine, Matthew G. Annis, Afnan Abu-Thuraia, Quebec Breast Cancer Foundation Tissue Microarray Consortium, Peter M. Siegel

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The Use of Multiplex Phosphorescence Analysis (PHOSPHAN^TM) and Polymerase Chain Reaction for Laboratory Diagnosis of Ixodid Tick-borne Borrelioses by T. I. Kuznetsova, V. G. Pomelova, E. I. Korenberg, N. S. Osin

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The Features of a Humoral Immune Response Development during the Acute Phase of ixodes Tick-Borne Borreliosis (Based on Multiplex Analysis with the Immunochip) by V. G. Pomelova, E. I. Korenberg, T. I. Kuznetsova, N. S. Osin

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Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data. by Darragh G McArt, Philip D Dunne, Jaine K Blayney, Manuel Salto-Tellez, Sandra Van Schaeybroeck, Peter W Hamilton, Shu-Dong Zhang

“…The advent of next generation sequencing technologies (NGS) has expanded the area of genomic research, offering high coverage and increased sensitivity over older microarray platforms. Although the current cost of next generation sequencing is still exceeding that of microarray approaches, the rapid advances in NGS will likely make it the platform of choice for future research in differential gene expression. …”
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A new method for analyzing gene expression data by PAN Hai-yan, ZHU Jun, HAN Dan-fu

“…Microarray technique provides a systematic genome-wide approach to solve a wide range of problems such as gene functions, gene regulations, and the disease diagnoses and treatments. …”
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Using rule-based machine learning for candidate disease gene prioritization and sample classification of cancer gene expression data. by Enrico Glaab, Jaume Bacardit, Jonathan M Garibaldi, Natalio Krasnogor

“…Microarray data analysis has been shown to provide an effective tool for studying cancer and genetic diseases. …”
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Sperm associated antigen 9 (SPAG9) a promising therapeutic target of ovarian carcinoma by Nirmala Jagadish, Rukhsar Fatima, Aditi Sharma, Sonika Devi, Vitusha Suri, Vikash Kumar, Anil Suri

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Evaluation of gene expression classification studies: factors associated with classification performance. by Putri W Novianti, Kit C B Roes, Marinus J C Eijkemans

“…Classification methods used in microarray studies for gene expression are diverse in the way they deal with the underlying complexity of the data, as well as in the technique used to build the classification model. …”
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Gene Expression Profiles for Predicting Metastasis in Breast Cancer: A Cross-Study Comparison of Classification Methods by Mark Burton, Mads Thomassen, Qihua Tan, Torben A. Kruse

“…Machine learning has increasingly been used with microarray gene expression data and for the development of classifiers using a variety of methods. …”
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Bioinformatics meets machine learning: identifying circulating biomarkers for vitiligo across blood and tissues by Qiyu Wang, Jingwei Yuan, Jingwei Yuan, Mengdi Zhang, Haiyan Jia, Hongjie Lu, Yan Wu

“…The merged microarray data were then used for WGCNA to identify modules of features genes. …”
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A RNA-Seq Analysis of the Rat Supraoptic Nucleus Transcriptome: Effects of Salt Loading on Gene Expression. by Kory R Johnson, C C T Hindmarch, Yasmmyn D Salinas, YiJun Shi, Michael Greenwood, See Ziau Hoe, David Murphy, Harold Gainer

“…In addition, we compare the SON transcriptomes resolved by RNA-Seq methods with the SON transcriptomes determined by Affymetrix microarray methods in rats under the same osmotic conditions, and find that there are 6,466 genes present in the SON that are represented in both data sets, although 1,040 of the expressed genes were found only in the microarray data, and 2,762 of the expressed genes are selectively found in the RNA-Seq data and not the microarray data. …”
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Systematic Omics Analysis Review (SOAR) tool to support risk assessment. by Emma R McConnell, Shannon M Bell, Ila Cote, Rong-Lin Wang, Edward J Perkins, Natàlia Garcia-Reyero, Ping Gong, Lyle D Burgoon

“…SOAR is a spreadsheet tool of 35 objective questions developed by domain experts, focused on transcriptomic microarray studies, and including four main topics: test system, test substance, experimental design, and microarray data. …”
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Identification of Differentially Expressed Genes and Elucidation of Pathophysiological Relevance of ABCA1 in HaCaT Cells Induced by PM2.5 by Fen Peng, Chen-Hong Xue, Xiao-Jing Yang, Jing-Yi Huang, Zhou Chen, Jian-Zhong Zhang

“…Cell cycle distribution and apoptosis were detected by flow cytometry. Microarray analyses were used to find out the microarray gene expression profiling; data processing included gene enrichment and pathway analysis. …”
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Effect of Garlic Organic Sulfides on Gene Expression Profiling in HepG2 Cells and Its Biological Function Analysis by Ingenuity Pathway Analysis System and Bio-Plex-Based Assays by Chenghao Lv, Caiqiong Wang, Ping Li, Yiwen Huang, Xiangyang Lu, Meng Shi, Chaoxi Zeng, Si Qin

“…RT-qPCR results indicated that the microarray data is trustworthy, and the structure-activity analysis data found that more sulfur atoms have more powerful properties; thus, microarray data of DTS was preceded to the subsequent IPA analysis. …”
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Knockdown of A-kinase anchor protein 4 inhibits proliferation of triple-negative breast cancer cells and by Nirmala Jagadish, Sonika Devi, Namita Gupta, Vitusha Suri, Anil Suri

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ChIP-chip designs to interrogate the genome of Xenopus embryos for transcription factor binding and epigenetic regulation. by Robert C Akkers, Simon J van Heeringen, J Robert Manak, Roland D Green, Hendrik G Stunnenberg, Gert Jan C Veenstra

“…<h4>Background</h4>Chromatin immunoprecipitation combined with genome tile path microarrays or deep sequencing can be used to study genome-wide epigenetic profiles and the transcription factor binding repertoire. …”
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Gene Expression Music Algorithm-Based Characterization of the Ewing Sarcoma Stem Cell Signature by Martin Sebastian Staege

“…Gene Expression Music Algorithm (GEMusicA) is a method for the transformation of DNA microarray data into melodies that can be used for the characterization of differentially expressed genes. …”
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Analysis of Crucial Genes and Pathways Associated with Spared Nerve Injury-Induced Neuropathic Pain by Dong Mao, Huang Zhai, Gang Zhao, Jingyi Mi, Yongjun Rui

“…Key genes like Nrg1 and Fgf9 in cluster 1, Timp1 in cluster 2, and Atf3 and C3 in cluster 3 were screened out after corroborating microarray data with other microarray data. Conclusions. …”
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